ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8680A>G (p.Ile2894Val)

gnomAD frequency: 0.00001  dbSNP: rs1272294316
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000711305 SCV000841646 uncertain significance not provided 2018-04-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001835935 SCV002177058 uncertain significance Cohen syndrome 2023-12-17 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2919 of the VPS13B protein (p.Ile2919Val). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 585722). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt VPS13B protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002369981 SCV002685090 uncertain significance Inborn genetic diseases 2018-03-10 criteria provided, single submitter clinical testing The p.I2919V variant (also known as c.8755A>G), located in coding exon 47 of the VPS13B gene, results from an A to G substitution at nucleotide position 8755. The isoleucine at codon 2919 is replaced by valine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001835935 SCV002082685 uncertain significance Cohen syndrome 2020-10-08 no assertion criteria provided clinical testing

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